To advance in this game, the player needs to play the story mode, where he/she will control Lucy Fleetfoot. She is sent by Professor P to stop Team Phobos Battalion, because they have stolen the Poké Balls to use its energy on Phobosfera.

On February 13th, 2014, a sequel titled Pokémon Battle Trozei was announced for release on March 20th 2014.